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SUPPORTRe: chain breaks

HEllo Christopher,

Yes, it looks true.

In the older version (pre-release of mod6 and older) chainbreaks are OK
in the alignment, in the current version (mod6v0) they cause problems.
Only those chainbreak characters, that are within a sequence, not the
ones, that separate heteroatoms.

On the other hand, you do not need to include them in the sequence,
Modeller will automatically assume a chain break, if there is a longer
than usual bond distance.

I hope,  removing chain breaks from your seq will make your top file
work, if not, let us know.

best wishes,


"Christopher A. Wells" wrote:
> I have been successfully using Mod4.0 to model multiple subunits
> together utilizing chain breaks in the alignment.
> However this is causing problems in Mod6.0.  I found in the manual for
> 6.0:
> "For the time being, this and other alignment commands remove chain
> break information from the CALN array..." p.59
> So this brings up several questions:
> 1) Is this the reason why I cannot create models with chain breaks in
> 6.0?
> 2) Is there an alternative solution besides sticking with Mod4.0 for the
> time being?
> 3) Is there an estimate on when chain breaks will be incorporated into
> Mod6.0?
> Thanks in advance,
> Christopher Wells
> MD/PhD Student
> Department of Pharmacology
> Medical University of South Carolina

Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras